From git at ins.uni-bonn.de  Wed Sep 10 00:28:02 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed, 10 Sep 2014 00:28:02 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch GUI_Fixes created.
	v1.4.7-13-g0741f4d
Message-ID: <20140909222802.6736310000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, GUI_Fixes has been created
        at  0741f4d175456b6ffd128ea624a7a20273533b6c (commit)

- Log -----------------------------------------------------------------
commit 0741f4d175456b6ffd128ea624a7a20273533b6c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Aug 20 14:38:24 2014 +0200

    FIX: new item is just to some default values in QtMoleculeList, filled later anway.

commit 86c0133532eb8e9d465ff746bcea0aecae8de1e6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 8 23:20:12 2014 +0200

    QMenu extended for tooltips, but not working yet.
    
    - somehow no QHelpEvents are triggered that would cause display of tooltips
      for QActions as menuitems.

commit 1631101c583989217756e201430f3b6f4e8c6e90
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 8 23:15:11 2014 +0200

    In QTUI Dialog window now has a meaningful title.
    
    - Dialog cstor now requires a title.
    - UIFactory::makeDialog() needs to be provided with this title.
    - Menu::populateActions() uses addAction with twice just the token.
    - Action::createDialog() provides title from its Traits.

commit 152e5c638ad572ebf3bef92b902419d5c7ca5504
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 8 21:33:39 2014 +0200

    FIX: Querys now have own description as tooltip, not Action's.

commit 0fe13544341ccb9e5f81e1da9701139c95742ec6
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 7 20:22:02 2014 +0200

    In QTUI empty dialogs no longer have to be confirmed.
    
    - this was already present but hasQueries() did always end up true as it also
      counted all EmptyQuery.
    - TESTFIX: Removed grep of description for regression test WarrantyAction as
      EmptyQuery is no longer handle()d.

commit 95cfacdff536aaf7fb3937c5b0656feb10da531c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 7 20:21:38 2014 +0200

    Added FileSuffixValidator to all Actions where missing but appropriate.
    
    - also clean up some unnecessary includes.

commit dae15830575cff1e67648579393887f666f06f35
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 7 19:44:06 2014 +0200

    FileQtQuery retrieves valid suffixes from validators.
    
    - added getFlatListFromHierarchyOfValidators() that steps through the hierarchy
      of validators and generates a flat vector with all matching types.
    - Or_Validatorm Not_Validator::getA(), ::getB() added. (present for And_...
      already).
    - FileSuffixValidator::getSuffix(), ParserFileValidator::getSuffixes() added.

commit ce4126dccd4487e1bb02f6582b75fc09fdf73408
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Aug 30 17:16:38 2014 +0200

    FIX: Added update mechanism to GLWorldScene when WorldTime changes.
    
    - bonds were not updated when WorldTime changed, atoms only change because each
      was subscribed to WorldTime.
    - Now, just GLWorldView is subscribed to WorldTime::TimeChanged, emitting
      TimeChanged and activating GLWorldScene::updated() signal.
    - GLWorldScene has access to private reset..() functions of
      GLMoleculeObject_atom and GLMoleculeObject_bond.
    - added GLWorldScene::update(), enhancing (also modified) ::init() function.
      It does not use molecules anymore, but directly the World's atoms. These
      are iterated over, checked whether already present and updated or added.
      Similarly with bonds. update() is activated on signal updated().

commit 8592c990d61a1b6a469219b569e217550fa13b6b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 26 09:40:55 2014 +0200

    FIX: GLMoleculeObject_shape might use empty point list for tesselation.
    
    - this causes segfault if a "nowhere" shape was created. Signal ShapedAdded
      causes tesselation of this shape and storing the mesh but the tesselation
      routine does not work if less than three points are given.
    - added check to Tesselation::operator() for at least three points.
    - MEMFIX: Tesselation object never deleted.

commit 42ffb581447753ba079ae9d6bec125084a90b079
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 15 15:27:55 2014 +0200

    FIX: BondGraph::cleanAdjacencyList() killed bonds of time steps before.
    
    - we use WorldTime's current time step only now.

commit dc798d46df2d2028d2fe5f96f29aac56230c6797
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 15 13:19:34 2014 +0200

    FIX: Removed some misleading output of CorrectBondDegreeAction.

commit 388dddec6195c09047052f2aef28f5ad6c39ce20
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 15 02:00:21 2014 +0200

    World::setTime() now only copies bond graph, does not re-create it.
    
    - this gives us more flexibility when doing MD/Opt because we may decice for
      ourselves whether we want to remain (within the fragmentation scheme) in
      the structure governed by the same bond graph ... or seek even for a
      different structure (although that's not so easy due to charge neutrality).

commit 553c546a9212dd6cedc74651403cde0e33e0c47f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 15 01:59:33 2014 +0200

    Added option keep-bondgraph to MolecularDynamicsAction and StructuralOptimizationAction.
    
    - this removes the actions to re-create the bond graph per MD/OPT step from
      the sequence of actions.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Wed Sep 10 10:11:49 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed, 10 Sep 2014 10:11:49 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Cleanup_old_code
	created. v1.4.7-13-g9d37d49
Message-ID: <20140910081150.1D20210000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "MoleCuilder".

The branch, Cleanup_old_code has been created
        at  9d37d49fb97beb7b4a04dad48e185202bd075fc9 (commit)

- Log -----------------------------------------------------------------
commit 9d37d49fb97beb7b4a04dad48e185202bd075fc9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 7 20:27:04 2014 +0200

    Removed lots of commented-out code from GLWorldView.

commit 6e12f56f8b65e5db654b2770b1225cd26839ab8f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 7 18:50:10 2014 +0200

    Removed PrepareClustersInWater().

commit a0da4fd1c122d8bc14eb9fb84be8446707bdea34
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 5 20:31:09 2014 +0200

    Moved and renamed SuspendInWaterAction from Molecule.. to FillAction/SuspendInMoleculeAction.
    
    - copied code from PrepareClustersInWater() and FillRegularGridAction as a
      start, not working yet.
    - TESTFIX: Removed -u from regression tests InvalidCommands as new
      SuspendInMoleculeAction no longer has any values without default values.

commit 54387c654375bc1ac220eb5077a0cd18314705b2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 1 17:57:23 2014 +0200

    Removed FillBoxWithMolecule(), FillVoidWithMolecule, and helper functions.
    
    - these are no longer needed as Actions have been removed.

commit cf2271f0f76b3b3923aa0fd41ab5b90569628694
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 1 17:54:30 2014 +0200

    Removed FillVoidWithMolecule and FillWithMolecule actions.
    
    - these can be replaced by FillRegularGrid/FillVolume and FillSurface.
    - TESTFIX: DipoleCorrelation used fill-void, replaced by fill-regular-grid.

commit 1c1a2d3a425370045c2e51ad34a8e120a5eecd1b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 3 21:11:14 2014 +0200

    Refactored FillSurfaceAction to also use FillerPreparators.
    
    - added ShapeSurfaceFillerPreparator for preparing the filler.
    - added new SurfaceRandomInserter for randomly translating filled-in molecule
      on shape's surface (no rotational randomness as RandomInserter cannot be
      forced to the alignment axis).
    - TESTFIX: renamed Filling regression folder SphericalSurface -> FillSurface.
    - TESTS: added FillSurface filling regression tests for every present shape.

commit d1ea5d6f228dd21f95414ad1fe8c5c9af52e361c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 3 20:00:26 2014 +0200

    Added FillVolumeAction for filling a Shape's volume.
    
    - added ShapeFillerPreparator for preparing the volume filler.
    - FIX: MeshAdaptor should include Mesh.hpp.
    - added regression tests for FillVolume for all present shapes.
    - all but cylinder fail because of missing implementation, are marked as
      XFAIL for the moment, except everywhere and nowhere of FillVolume which say
      they fail explicitly. (this is not an implementation problem, for these
      shapes filling makes no sense.)

commit 36f45c7566bcbd1eab7647b44689588ab0fb839c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 4 17:30:59 2014 +0200

    FIX: Renamed testsuite-molecules-fill-.. -> testsuite-fill-.. in Filling/.

commit cae61447a8c102b09ec82b970c3991c54f311fb5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 2 17:06:31 2014 +0200

    Extracted filler preparing functionality from FillRegularGridAction.
    
    - initialization functions placed into BaseFillerPreparator and derived
      BoxFillerPreparator.
    - slimmed down FillRegularGridAction.
    - DOCU: Extended documentation on new FillerPreparators.

commit a090e3bbbb29271069f6efbe5ae41f0b9d0dcd57
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 15 14:46:54 2014 +0200

    FIX: FillRegularGridAction requires filler molecule at origin.
    
    - FillRegularGridAction uses CenterEdge as does FillRegularSurface.
    - TESTFIX: coordinates shifted by z=0.504 because filler water molecule was not
      centered at origin before (and not fully inside positive octant either).

commit 833b155e089160225200039831a7742be7bb1a16
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 1 17:54:02 2014 +0200

    FIX: Changes to function signatures in molecule_geometry.
    
    - no more returning allocated pointer (Vector *)
    - no more Pointers as parameters.
    - removed functions that are only convenience and have nothing to do with the
      molecule.
    - changes elsewhere due to signature changes.

commit 2d701e7056fe4b1af51c7f20e51cc77ee82ff91b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Aug 20 14:36:11 2014 +0200

    FIX: molecule::Translate() used in CenterInBox(), CenterEdge(), CenterPeriodic(), and CenterAtVector().

commit 40bb9e2215e41bb1d3b215cb9b5ae55b04153352
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 17 12:10:53 2014 +0200

    FIX: molecule::Translate() uses AtomSet directly.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Wed Sep 10 21:57:54 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed, 10 Sep 2014 21:57:54 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Cleanup_old_code
	deleted. v1.4.7-13-g9d37d49
Message-ID: <20140910195754.7476910000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "MoleCuilder".

The branch, Cleanup_old_code has been deleted
       was  9d37d49fb97beb7b4a04dad48e185202bd075fc9

-----------------------------------------------------------------------
9d37d49fb97beb7b4a04dad48e185202bd075fc9 Removed lots of commented-out code from GLWorldView.
-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Wed Sep 10 21:57:59 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed, 10 Sep 2014 21:57:59 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Cleanup_old_code
	created. v1.4.7-13-g5a9f4c1
Message-ID: <20140910195759.C6AB310000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "MoleCuilder".

The branch, Cleanup_old_code has been created
        at  5a9f4c1e1caa72f88ad756fdaa11851f54a9426b (commit)

- Log -----------------------------------------------------------------
commit 5a9f4c1e1caa72f88ad756fdaa11851f54a9426b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 7 20:27:04 2014 +0200

    Removed lots of commented-out code from GLWorldView.

commit 2b7375290eb8729da103864ee7aab10467ed3346
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 7 18:50:10 2014 +0200

    Removed PrepareClustersInWater().

commit aa55d00dbcc8c34ecf6c22c2d29232d84d0cc262
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 5 20:31:09 2014 +0200

    Moved and renamed SuspendInWaterAction from Molecule.. to FillAction/SuspendInMoleculeAction.
    
    - copied code from PrepareClustersInWater() and FillRegularGridAction as a
      start, not working yet.
    - TESTFIX: Removed -u from regression tests InvalidCommands as new
      SuspendInMoleculeAction no longer has any values without default values.

commit 2528d8462c54c9cdfb2d41b92bd6e34d9fd0c364
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 1 17:57:23 2014 +0200

    Removed FillBoxWithMolecule(), FillVoidWithMolecule, and helper functions.
    
    - these are no longer needed as Actions have been removed.

commit 16c7dd3fc6c66022b4b13c912de169a1f812196c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 1 17:54:30 2014 +0200

    Removed FillVoidWithMolecule and FillWithMolecule actions.
    
    - these can be replaced by FillRegularGrid/FillVolume and FillSurface.
    - TESTFIX: DipoleCorrelation used fill-void, replaced by fill-regular-grid.

commit df9f200764a5636d8eb51224f34c27dbd7463b9a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 3 21:11:14 2014 +0200

    Refactored FillSurfaceAction to also use FillerPreparators.
    
    - added ShapeSurfaceFillerPreparator for preparing the filler.
    - added new SurfaceRandomInserter for randomly translating filled-in molecule
      on shape's surface (no rotational randomness as RandomInserter cannot be
      forced to the alignment axis).
    - TESTFIX: renamed Filling regression folder SphericalSurface -> FillSurface.
    - TESTS: added FillSurface filling regression tests for every present shape,
      we let everywhere and nowhere fail hard in performCall(), as this works also
      with disable-debug.

commit 6801f4f3b7ed127fa9a9c8afe64f82d34df963d2
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 3 20:00:26 2014 +0200

    Added FillVolumeAction for filling a Shape's volume.
    
    - added ShapeFillerPreparator for preparing the volume filler.
    - FIX: MeshAdaptor should include Mesh.hpp.
    - added regression tests for FillVolume for all present shapes.
    - all but cylinder fail because of missing implementation, are marked as
      XFAIL for the moment, except everywhere and nowhere of FillVolume which say
      they fail explicitly. (this is not an implementation problem, for these
      shapes filling makes no sense.) We explicitly check for the currently failing
      shape types and let the Action fail (cause this works also in disable-debug).

commit 36f45c7566bcbd1eab7647b44689588ab0fb839c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 4 17:30:59 2014 +0200

    FIX: Renamed testsuite-molecules-fill-.. -> testsuite-fill-.. in Filling/.

commit cae61447a8c102b09ec82b970c3991c54f311fb5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 2 17:06:31 2014 +0200

    Extracted filler preparing functionality from FillRegularGridAction.
    
    - initialization functions placed into BaseFillerPreparator and derived
      BoxFillerPreparator.
    - slimmed down FillRegularGridAction.
    - DOCU: Extended documentation on new FillerPreparators.

commit a090e3bbbb29271069f6efbe5ae41f0b9d0dcd57
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 15 14:46:54 2014 +0200

    FIX: FillRegularGridAction requires filler molecule at origin.
    
    - FillRegularGridAction uses CenterEdge as does FillRegularSurface.
    - TESTFIX: coordinates shifted by z=0.504 because filler water molecule was not
      centered at origin before (and not fully inside positive octant either).

commit 833b155e089160225200039831a7742be7bb1a16
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 1 17:54:02 2014 +0200

    FIX: Changes to function signatures in molecule_geometry.
    
    - no more returning allocated pointer (Vector *)
    - no more Pointers as parameters.
    - removed functions that are only convenience and have nothing to do with the
      molecule.
    - changes elsewhere due to signature changes.

commit 2d701e7056fe4b1af51c7f20e51cc77ee82ff91b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Aug 20 14:36:11 2014 +0200

    FIX: molecule::Translate() used in CenterInBox(), CenterEdge(), CenterPeriodic(), and CenterAtVector().

commit 40bb9e2215e41bb1d3b215cb9b5ae55b04153352
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 17 12:10:53 2014 +0200

    FIX: molecule::Translate() uses AtomSet directly.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Mon Sep 15 13:51:25 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon, 15 Sep 2014 13:51:25 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch MemFixes created.
	v1.4.7-16-gb4d77c0
Message-ID: <20140915115125.59AEF10000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
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The branch, MemFixes has been created
        at  b4d77c0ac2e204573b6a9ae78bdbeddbfca1dd96 (commit)

- Log -----------------------------------------------------------------
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From git at ins.uni-bonn.de  Mon Sep 15 13:53:07 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon, 15 Sep 2014 13:53:07 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch MemFixes deleted.
	v1.4.7-16-gb4d77c0
Message-ID: <20140915115308.0193210000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "MoleCuilder".

The branch, MemFixes has been deleted
       was  b4d77c0ac2e204573b6a9ae78bdbeddbfca1dd96

-----------------------------------------------------------------------
b4d77c0ac2e204573b6a9ae78bdbeddbfca1dd96 DOCU: Update on test policy with respect to now working valgrind tests.
-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Mon Sep 15 13:53:11 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon, 15 Sep 2014 13:53:11 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch MemFixes created.
	v1.4.7-17-g5524ae9
Message-ID: <20140915115311.62D0310000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "MoleCuilder".

The branch, MemFixes has been created
        at  5524ae96797a4fa7244c906512ec2bde76c952b3 (commit)

- Log -----------------------------------------------------------------
commit 5524ae96797a4fa7244c906512ec2bde76c952b3
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 29 11:43:10 2014 +0200

    DOCU: Update on test policy with respect to now working valgrind tests.

commit 8d4eaa3c9914c99397ccf2583e276838c176a082
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sat Aug 30 15:25:53 2014 +0200

    MEMFIX: ElementDbAction would loose memory when parsing command-line arguments failed.
    
    - UndoState was allocated too early.

commit 11d433d190a134a3015b4de85d3738c20a307688
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 29 11:44:20 2014 +0200

    MEMFIX: ActionQueue was not stopped() when argument parsing failed.
    
    - this just caused an exception and the ActionQueue thread would be aborted
      uncleanly. This is only affected --enable-action-thread.
    - CommandLineParser calls ActionQueue::stop() on catching exception.
    - CommandLineParser also rethrows std::exception when parsing of command-line
      arguments went wrong (not faulty but completely missing values).
    - ActionQueue uses exitflag of 134 on std::exception.

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From git at ins.uni-bonn.de  Mon Sep 15 13:54:30 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon, 15 Sep 2014 13:54:30 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch ThreadFixes deleted.
	v1.4.7-17-g38074bf
Message-ID: <20140915115430.5CA6C10000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, ThreadFixes has been deleted
       was  38074bf6c963bbf4bc326b7725ba73b8eccd79f4

-----------------------------------------------------------------------
38074bf6c963bbf4bc326b7725ba73b8eccd79f4 THREADFIX: Fixed ActionQueue with respect to mutex and threads.
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From git at ins.uni-bonn.de  Mon Sep 15 13:54:33 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon, 15 Sep 2014 13:54:33 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch ThreadFixes created.
	v1.4.7-20-g2b11dfb
Message-ID: <20140915115433.F11D610000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "MoleCuilder".

The branch, ThreadFixes has been created
        at  2b11dfbc1e1e35a26b0f0634b74d579dc3fc208b (commit)

- Log -----------------------------------------------------------------
commit 2b11dfbc1e1e35a26b0f0634b74d579dc3fc208b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 3 21:26:17 2014 +0200

    Cleaned up use of mutexes in ActionQueue.
    
    - tempqueue now has its own mutex.
    - more often using lock_guard.
    - run_thread_isIdle has own mutex.

commit 13102c09392ef451c7547ec206917e96beeb1fad
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 3 19:21:08 2014 +0200

    Added extra flag run_thread_running to ActionQueue.
    
    - helgrind admonished race conditions when thread is joined. This did not fix
      them but should be safer as we cannot know whether the other thread has
      already been started when suddenly shutting down molecuilder due to an
      exception.

commit bc2d4676ddd23758665398fbacb74e40e7fdb45b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 29 11:46:02 2014 +0200

    THREADFIX: Fixed ActionQueue with respect to mutex and threads.
    
    - run_thread is now last member variable, hence started after all other
      variables are initialized.
    - separated accesses to queues and to run_thread_isIdle flag. Also renamed
      its mutex for easier association with it.

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From git at ins.uni-bonn.de  Mon Sep 15 14:01:02 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon, 15 Sep 2014 14:01:02 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.7
	deleted. v1.4.7
Message-ID: <20140915120102.C9E7A10000FA@jupiter.ins.uni-bonn.de>

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The branch, Candidate_v1.4.7 has been deleted
       was  29b35efc972c36f104ccae2ad8b50ce095b475e8

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29b35efc972c36f104ccae2ad8b50ce095b475e8 Set version to 1.4.7.
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From git at ins.uni-bonn.de  Mon Sep 15 14:03:56 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon, 15 Sep 2014 14:03:56 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch GUI_Fixes updated.
	v1.4.7-18-g8859b5e
Message-ID: <20140915120357.471C010000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, GUI_Fixes has been updated
       via  8859b5e80aaacf810ed6de2750789019357f0fa0 (commit)
       via  29b52b1607551f45b84d99fb44f6e5e121221626 (commit)
       via  9bdcc9b9d75a09f2bb7ddfba50b34f7ad62a7e68 (commit)
       via  0ac3e3aeb53bc6b57899974dd8ec414158ffaccc (commit)
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      from  0741f4d175456b6ffd128ea624a7a20273533b6c (commit)

Those revisions listed above that are new to this repository have
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- Log -----------------------------------------------------------------
commit 8859b5e80aaacf810ed6de2750789019357f0fa0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 12 10:00:59 2014 +0200

    Added QtFavoriteActions to QtToolBar to spawn placeholder icons of most favorite Actions.

commit 29b52b1607551f45b84d99fb44f6e5e121221626
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 12 10:00:16 2014 +0200

    Made ActionQueue observable.
    
    - has channel ActionQueued.
    - this is preparatory to know about most used Actions.

commit 9bdcc9b9d75a09f2bb7ddfba50b34f7ad62a7e68
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 11 22:55:47 2014 +0200

    FIX: QtHomologyList lacked use of FunctionModel::filter_t to split up arguments.
    
    - we need to split up the vector of arguments into lists of argument tuples
      that each potential can digest. And these tuples are different per potential.

commit 0ac3e3aeb53bc6b57899974dd8ec414158ffaccc
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 11 09:30:53 2014 +0200

    FIX: QSeisPlotPage takes up all remaining space in QtHomologyList.
    
    - thanks to http://stackoverflow.com/questions/11911323/how-to-allow-a-qwidget-to-expand-to-an-entire-tab-within-a-qtabwidget

commit f8bccc9d2f41fb1866651aadba4beab9fe0bea1d
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 11 00:12:17 2014 +0200

    FIX: QtQueryList now works with pointers, FileQtQuery gives name of file.
    
    - FileQtQuery always said "input-file:" which becomes ambigious when multiple
      files are queried in a single dialog.
    - Value_string was a specialization for string type. This was used to also
      specialize for element type (and also for atom and molecule type).
    - This automatically fixes problems where QtQueryList would show memory
      addresses in the list instead of e.g. element names. This occurs because
      toString() is used on the pointer, now getName() is called.

-----------------------------------------------------------------------

Summary of changes:
 src/Actions/ActionQueue.cpp                        |   15 ++-
 src/Actions/ActionQueue.hpp                        |   29 +++-
 src/Parameters/Makefile.am                         |   26 ++-
 .../Specifics/Value_atom.cpp}                      |   63 ++++---
 src/Parameters/Specifics/Value_atom.hpp            |   33 ++++
 .../Specifics/Value_element.cpp}                   |   52 +++---
 src/Parameters/Specifics/Value_element.hpp         |   33 ++++
 src/Parameters/Specifics/Value_molecule.cpp        |   76 ++++++++
 src/Parameters/Specifics/Value_molecule.hpp        |   33 ++++
 src/Parameters/{ => Specifics}/Value_string.cpp    |    6 +
 src/Parameters/{ => Specifics}/Value_string.hpp    |    3 +
 src/Parameters/Value.hpp                           |    5 +-
 src/UIElements/Makefile.am                         |    1 +
 src/UIElements/Qt4/QtMainWindow.cpp                |    1 +
 src/UIElements/Qt4/Query/FileQtQuery.cpp           |    2 +-
 src/UIElements/Views/Qt4/Plotting/QSeisPlot.cpp    |    2 +-
 src/UIElements/Views/Qt4/QtHomologyList.cpp        |   44 +++--
 src/UIElements/Views/Qt4/QtToolBar.cpp             |   11 +-
 src/UIElements/Views/Qt4/QtToolBar.hpp             |   74 +++++++-
 .../Views/Qt4/QtToolBar_QtFavoriteActions.cpp      |  199 ++++++++++++++++++++
 20 files changed, 619 insertions(+), 89 deletions(-)
 copy src/{Fragmentation/Exporters/unittests/stubs/SaturatedBondStub.cpp => Parameters/Specifics/Value_atom.cpp} (52%)
 create mode 100644 src/Parameters/Specifics/Value_atom.hpp
 copy src/{Actions/toPythonString.cpp => Parameters/Specifics/Value_element.cpp} (52%)
 create mode 100644 src/Parameters/Specifics/Value_element.hpp
 create mode 100644 src/Parameters/Specifics/Value_molecule.cpp
 create mode 100644 src/Parameters/Specifics/Value_molecule.hpp
 rename src/Parameters/{ => Specifics}/Value_string.cpp (92%)
 rename src/Parameters/{ => Specifics}/Value_string.hpp (83%)
 create mode 100644 src/UIElements/Views/Qt4/QtToolBar_QtFavoriteActions.cpp


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From git at ins.uni-bonn.de  Mon Sep 15 18:43:37 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon, 15 Sep 2014 18:43:37 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.8
	created. v1.4.7-52-gf07f16f
Message-ID: <20140915164337.F237C10000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "MoleCuilder".

The branch, Candidate_v1.4.8 has been created
        at  f07f16f1f6208dafd208ae54ed2ec9fdc2331b5f (commit)

- Log -----------------------------------------------------------------
commit f07f16f1f6208dafd208ae54ed2ec9fdc2331b5f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 17:06:47 2014 +0200

    Set version to 1.4.8.
    
    - MoleCuilder library is now 14:1:0.
    - Codename "" ().

commit 7f1b51d9ebdfbd81ece2b0afc41b3153a06c5e91
Merge: b73545e 8859b5e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 17:05:28 2014 +0200

    Merge branch 'GUI_Fixes' into stable

commit b73545e66c148c8d0fce990a5e3138a99fadcc28
Merge: 55736be 5524ae9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 16:28:50 2014 +0200

    Merge branch 'MemFixes' into stable
    
    Conflicts:
    	src/Tesselation/boundary.cpp
    
    - Lots of functions removed in boundary.cpp in Cleanup_old_code but seemingly
      also affected during MemFixes.

commit 55736be799388502de9a57ac542d215e5ce0565a
Merge: 29b35ef 5a9f4c1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 16:22:29 2014 +0200

    Merge branch 'Cleanup_old_code' into stable

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Mon Sep 15 23:49:09 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon, 15 Sep 2014 23:49:09 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.8
	deleted. v1.4.7-52-gf07f16f
Message-ID: <20140915214909.A2D7F10000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, Candidate_v1.4.8 has been deleted
       was  f07f16f1f6208dafd208ae54ed2ec9fdc2331b5f

-----------------------------------------------------------------------
f07f16f1f6208dafd208ae54ed2ec9fdc2331b5f Set version to 1.4.8.
-----------------------------------------------------------------------


hooks/post-receive
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From git at ins.uni-bonn.de  Mon Sep 15 23:49:37 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Mon, 15 Sep 2014 23:49:37 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.8
	created. v1.4.7-53-g05341a0
Message-ID: <20140915214937.2E9BE10000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, Candidate_v1.4.8 has been created
        at  05341a09115eb72edd1ad3c7350702234bb2fa73 (commit)

- Log -----------------------------------------------------------------
commit 05341a09115eb72edd1ad3c7350702234bb2fa73
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 17:06:47 2014 +0200

    Set version to 1.4.8.
    
    - MoleCuilder library is now 14:1:0.
    - Codename "" ().

commit 7e1a886b77240a61da6f1d0f312f69d0910ff9f0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 23:29:05 2014 +0200

    MEMFIX: Thrown ParserException causes mem leak in LoadAction
    
    - also added catching of exception to both LoadAction and InputAction.

commit 7f1b51d9ebdfbd81ece2b0afc41b3153a06c5e91
Merge: b73545e 8859b5e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 17:05:28 2014 +0200

    Merge branch 'GUI_Fixes' into stable

commit b73545e66c148c8d0fce990a5e3138a99fadcc28
Merge: 55736be 5524ae9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 16:28:50 2014 +0200

    Merge branch 'MemFixes' into stable
    
    Conflicts:
    	src/Tesselation/boundary.cpp
    
    - Lots of functions removed in boundary.cpp in Cleanup_old_code but seemingly
      also affected during MemFixes.

commit 55736be799388502de9a57ac542d215e5ce0565a
Merge: 29b35ef 5a9f4c1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 16:22:29 2014 +0200

    Merge branch 'Cleanup_old_code' into stable

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Tue Sep 16 02:12:34 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Tue, 16 Sep 2014 02:12:34 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.8
	deleted. v1.4.7-53-g05341a0
Message-ID: <20140916001234.DFE4D10000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, Candidate_v1.4.8 has been deleted
       was  05341a09115eb72edd1ad3c7350702234bb2fa73

-----------------------------------------------------------------------
05341a09115eb72edd1ad3c7350702234bb2fa73 Set version to 1.4.8.
-----------------------------------------------------------------------


hooks/post-receive
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From git at ins.uni-bonn.de  Tue Sep 16 02:12:38 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Tue, 16 Sep 2014 02:12:38 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.8
	created. v1.4.7-54-g586f10c
Message-ID: <20140916001238.C511710000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, Candidate_v1.4.8 has been created
        at  586f10c83860e32bd4385827fe0c3e97d2ba55cf (commit)

- Log -----------------------------------------------------------------
commit 586f10c83860e32bd4385827fe0c3e97d2ba55cf
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 17:06:47 2014 +0200

    Set version to 1.4.8.
    
    - MoleCuilder library is now 14:1:0.
    - Codename "" ().

commit ddfbd403ac839c27e59df6bc1810504ffec4fa86
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 16 02:09:36 2014 +0200

    FIX: CommandLineParser causes idling thread when parsing goes wrong.
    
    - CommandLineParser::Parse() now returns bool to give status of parsing, only
      when true is scanForArguments() called, which fills the ActionQueue's queue
      which is not executed anymore because the run thread was already stopped by
      the caught exception from the parse failure.

commit 7e1a886b77240a61da6f1d0f312f69d0910ff9f0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 23:29:05 2014 +0200

    MEMFIX: Thrown ParserException causes mem leak in LoadAction
    
    - also added catching of exception to both LoadAction and InputAction.

commit 7f1b51d9ebdfbd81ece2b0afc41b3153a06c5e91
Merge: b73545e 8859b5e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 17:05:28 2014 +0200

    Merge branch 'GUI_Fixes' into stable

commit b73545e66c148c8d0fce990a5e3138a99fadcc28
Merge: 55736be 5524ae9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 16:28:50 2014 +0200

    Merge branch 'MemFixes' into stable
    
    Conflicts:
    	src/Tesselation/boundary.cpp
    
    - Lots of functions removed in boundary.cpp in Cleanup_old_code but seemingly
      also affected during MemFixes.

commit 55736be799388502de9a57ac542d215e5ce0565a
Merge: 29b35ef 5a9f4c1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 16:22:29 2014 +0200

    Merge branch 'Cleanup_old_code' into stable

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Tue Sep 16 08:21:26 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Tue, 16 Sep 2014 08:21:26 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.8
	deleted. v1.4.7-54-g586f10c
Message-ID: <20140916062126.6001610000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
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The branch, Candidate_v1.4.8 has been deleted
       was  586f10c83860e32bd4385827fe0c3e97d2ba55cf

-----------------------------------------------------------------------
586f10c83860e32bd4385827fe0c3e97d2ba55cf Set version to 1.4.8.
-----------------------------------------------------------------------


hooks/post-receive
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From git at ins.uni-bonn.de  Tue Sep 16 08:21:32 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Tue, 16 Sep 2014 08:21:32 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.8
	created. v1.4.7-54-g4d966a0
Message-ID: <20140916062132.A153810000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
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The branch, Candidate_v1.4.8 has been created
        at  4d966a045dba17945ab7e6433ebf4faea3d73b17 (commit)

- Log -----------------------------------------------------------------
commit 4d966a045dba17945ab7e6433ebf4faea3d73b17
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 17:06:47 2014 +0200

    Set version to 1.4.8.
    
    - MoleCuilder library is now 14:1:0.
    - Codename "" ().

commit 06b5dfa95337fee961ce3018c5e56e6b64c06454
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 16 02:09:36 2014 +0200

    FIX: CommandLineParser causes idling thread when parsing goes wrong.
    
    - CommandLineParser::Parse() now returns bool to give status of parsing, only
      when true is scanForArguments() called, which fills the ActionQueue's queue
      which is not executed anymore because the run thread was already stopped by
      the caught exception from the parse failure.

commit 7e1a886b77240a61da6f1d0f312f69d0910ff9f0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 23:29:05 2014 +0200

    MEMFIX: Thrown ParserException causes mem leak in LoadAction
    
    - also added catching of exception to both LoadAction and InputAction.

commit 7f1b51d9ebdfbd81ece2b0afc41b3153a06c5e91
Merge: b73545e 8859b5e
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 17:05:28 2014 +0200

    Merge branch 'GUI_Fixes' into stable

commit b73545e66c148c8d0fce990a5e3138a99fadcc28
Merge: 55736be 5524ae9
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 16:28:50 2014 +0200

    Merge branch 'MemFixes' into stable
    
    Conflicts:
    	src/Tesselation/boundary.cpp
    
    - Lots of functions removed in boundary.cpp in Cleanup_old_code but seemingly
      also affected during MemFixes.

commit 55736be799388502de9a57ac542d215e5ce0565a
Merge: 29b35ef 5a9f4c1
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 16:22:29 2014 +0200

    Merge branch 'Cleanup_old_code' into stable

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Wed Sep 17 21:51:31 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed, 17 Sep 2014 21:51:31 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch stable updated.
	v1.4.7-54-g7f6a2fc
Message-ID: <20140917195131.4439C10000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, stable has been updated
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      from  29b35efc972c36f104ccae2ad8b50ce095b475e8 (commit)

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- Log -----------------------------------------------------------------
commit 7f6a2fc9f64c88371654df745552167f0e0e3a9c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 15 17:06:47 2014 +0200

    Set version to 1.4.8.
    
    - MoleCuilder library is now 14:1:0.
    - Codename "Correction Enterprises" (Paragraph 148-128 of US law decrees
      enterprises employing incarcerated offenders have to be known as such).

-----------------------------------------------------------------------

Summary of changes:
 LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp  |    2 +-
 LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp  |    2 +
 .../src/LinearAlgebra/RealSpaceMatrix.hpp          |    5 +-
 LinearAlgebra/src/LinearAlgebra/VectorContent.cpp  |    4 +-
 configure.ac                                       |    6 +-
 src/Actions/Action.cpp                             |    2 +-
 src/Actions/ActionQueue.cpp                        |   65 +-
 src/Actions/ActionQueue.hpp                        |   40 +-
 src/Actions/Action_impl_pre.hpp                    |    8 +-
 .../DipoleAngularCorrelationAction.cpp             |    4 +-
 .../AnalysisAction/DipoleCorrelationAction.cpp     |    4 +-
 .../AnalysisAction/PairCorrelationAction.cpp       |    4 +-
 .../AnalysisAction/PointCorrelationAction.cpp      |    4 +-
 .../AnalysisAction/SurfaceCorrelationAction.cpp    |    4 +-
 .../CommandAction/BondLengthTableAction.def        |    4 +-
 src/Actions/CommandAction/ElementDbAction.cpp      |    8 +-
 src/Actions/CommandAction/ElementDbAction.def      |    1 +
 src/Actions/CommandAction/LoadSessionAction.def    |    4 +-
 src/Actions/CommandAction/StoreSessionAction.def   |    4 +-
 src/Actions/FillAction/FillRegularGridAction.cpp   |  162 +-
 src/Actions/FillAction/FillSurfaceAction.cpp       |   79 +-
 src/Actions/FillAction/FillSurfaceAction.def       |   15 +-
 src/Actions/FillAction/FillVolumeAction.cpp        |  225 ++
 src/Actions/FillAction/FillVolumeAction.def        |   52 +
 src/Actions/FillAction/FillVolumeAction.hpp        |   22 +
 src/Actions/FillAction/SuspendInMoleculeAction.cpp |  333 +++
 src/Actions/FillAction/SuspendInMoleculeAction.def |   52 +
 src/Actions/FillAction/SuspendInMoleculeAction.hpp |   22 +
 .../ClearFragmentationResultsAction.def            |    8 -
 .../MolecularDynamicsAction.cpp                    |   23 +
 .../MolecularDynamicsAction.def                    |   11 +-
 .../StructuralOptimizationAction.cpp               |   23 +
 .../StructuralOptimizationAction.def               |   11 +-
 src/Actions/GlobalListOfActions.hpp                |    5 +-
 .../GraphAction/CorrectBondDegreeAction.cpp        |    8 -
 src/Actions/Makefile.am                            |   21 +-
 src/Actions/MoleculeAction/CopyAction.cpp          |    7 +-
 .../MoleculeAction/FillVoidWithMoleculeAction.cpp  |  166 --
 .../MoleculeAction/FillVoidWithMoleculeAction.def  |   49 -
 .../MoleculeAction/FillVoidWithMoleculeAction.hpp  |   22 -
 .../MoleculeAction/FillWithMoleculeAction.cpp      |  170 --
 .../MoleculeAction/FillWithMoleculeAction.def      |   53 -
 .../MoleculeAction/FillWithMoleculeAction.hpp      |   22 -
 .../MoleculeAction/ForceAnnealingAction.def        |    3 +-
 src/Actions/MoleculeAction/LoadAction.cpp          |   10 +-
 .../RotateAroundSelfByAngleAction.cpp              |   21 +-
 .../MoleculeAction/SuspendInWaterAction.cpp        |   92 -
 .../MoleculeAction/SuspendInWaterAction.def        |   37 -
 .../MoleculeAction/SuspendInWaterAction.hpp        |   22 -
 .../MoleculeAction/VerletIntegrationAction.def     |    2 +-
 src/Actions/PotentialAction/FitPotentialAction.cpp |   10 +-
 src/Actions/PotentialAction/FitPotentialAction.def |    5 +-
 src/Actions/Process.cpp                            |    5 +-
 src/Actions/WorldAction/InputAction.cpp            |    9 +-
 src/Actions/unittests/stubs/DummyUI.hpp            |    6 +-
 src/Analysis/analysis_correlation.cpp              |    7 -
 src/Analysis/unittests/CountBondsUnitTest.cpp      |   52 +-
 src/Box.cpp                                        |    2 +-
 src/Box.hpp                                        |    2 +-
 src/Filling/Inserter/SurfaceRandomInserter.cpp     |  100 +
 src/Filling/Inserter/SurfaceRandomInserter.hpp     |   48 +
 src/Filling/Makefile.am                            |   15 +-
 src/Filling/Mesh/MeshAdaptor.hpp                   |    1 +
 src/Filling/Preparators/BaseFillerPreparator.cpp   |  140 +
 src/Filling/Preparators/BaseFillerPreparator.hpp   |   75 +
 src/Filling/Preparators/BoxFillerPreparator.cpp    |   57 +
 src/Filling/Preparators/BoxFillerPreparator.hpp    |   42 +
 .../Preparators/ShapeSurfaceFillerPreparator.cpp   |   96 +
 .../Preparators/ShapeSurfaceFillerPreparator.hpp   |   49 +
 .../Preparators/ShapeVolumeFillerPreparator.cpp    |   64 +
 .../Preparators/ShapeVolumeFillerPreparator.hpp    |   37 +
 .../Exporters/SaturationDistanceMaximizer.cpp      |    5 +-
 src/Fragmentation/Homology/HomologyContainer.hpp   |    7 +
 src/Graph/BondGraph.hpp                            |   12 +-
 src/LinkedCell/linkedcell.cpp                      |   13 +-
 src/LinkedCell/unittests/linkedcellUnitTest.cpp    |    2 +-
 src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp |    2 +-
 src/Parameters/Makefile.am                         |   27 +-
 src/Parameters/Specifics/Value_atom.cpp            |   76 +
 src/Parameters/Specifics/Value_atom.hpp            |   33 +
 src/Parameters/Specifics/Value_element.cpp         |   73 +
 src/Parameters/Specifics/Value_element.hpp         |   33 +
 src/Parameters/Specifics/Value_molecule.cpp        |   76 +
 src/Parameters/Specifics/Value_molecule.hpp        |   33 +
 src/Parameters/Specifics/Value_string.cpp          |   57 +
 src/Parameters/Specifics/Value_string.hpp          |   29 +
 src/Parameters/Validators/Ops_Validator_impl.hpp   |   10 +
 .../Validators/Specific/FileSuffixValidator.hpp    |    3 +
 .../Validators/Specific/ParserFileValidator.cpp    |   10 +-
 .../Validators/Specific/ParserFileValidator.hpp    |    3 +
 src/Parameters/Validators/Validator.hpp            |    1 -
 .../getFlatListFromHierarchyOfValidators.hpp       |   59 +
 src/Parameters/Value.hpp                           |    5 +-
 src/Parameters/Value_string.cpp                    |   51 -
 src/Parameters/Value_string.hpp                    |   26 -
 src/Parser/PdbParser.cpp                           |    2 +-
 src/Potentials/PartialNucleiChargeFitter.cpp       |   16 +-
 src/Potentials/PotentialRegistry.cpp               |    4 +
 src/Potentials/PotentialRegistry.hpp               |    2 +-
 src/Potentials/SerializablePotential.hpp           |    2 +-
 src/Tesselation/CandidateForTesselation.cpp        |    2 +-
 src/Tesselation/boundary.cpp                       |  789 +------
 src/Tesselation/boundary.hpp                       |    3 -
 src/Tesselation/tesselation.cpp                    |   18 +-
 src/UIElements/CommandLineUI/CommandLineDialog.cpp |    3 +-
 src/UIElements/CommandLineUI/CommandLineDialog.hpp |    2 +-
 src/UIElements/CommandLineUI/CommandLineParser.cpp |   40 +-
 src/UIElements/CommandLineUI/CommandLineParser.hpp |    2 +-
 .../CommandLineUI/CommandLineUIFactory.cpp         |    4 +-
 .../CommandLineUI/CommandLineUIFactory.hpp         |    2 +-
 src/UIElements/Dialog.cpp                          |   11 +-
 src/UIElements/Dialog.hpp                          |    2 +-
 src/UIElements/Makefile.am                         |    2 +
 src/UIElements/Menu/Menu.cpp                       |    7 +-
 src/UIElements/Menu/Menu.hpp                       |   43 +-
 src/UIElements/Menu/Qt4/QMenu_tooltip.hpp          |   48 +
 src/UIElements/Menu/Qt4/QtMenu.hpp                 |   11 +-
 src/UIElements/Qt4/QtDialog.cpp                    |    6 +-
 src/UIElements/Qt4/QtDialog.hpp                    |    2 +-
 src/UIElements/Qt4/QtMainWindow.cpp                |    1 +
 src/UIElements/Qt4/QtUIFactory.cpp                 |    4 +-
 src/UIElements/Qt4/QtUIFactory.hpp                 |    2 +-
 src/UIElements/Qt4/Query/AtomsQtQuery.cpp          |    2 +-
 src/UIElements/Qt4/Query/DoublesQtQuery.cpp        |    2 +-
 src/UIElements/Qt4/Query/ElementsQtQuery.cpp       |    2 +-
 src/UIElements/Qt4/Query/FileQtQuery.cpp           |   52 +-
 src/UIElements/Qt4/Query/FilesQtQuery.cpp          |    2 +-
 src/UIElements/Qt4/Query/IntsQtQuery.cpp           |    2 +-
 src/UIElements/Qt4/Query/MoleculesQtQuery.cpp      |    2 +-
 src/UIElements/Qt4/Query/QtQuery.hpp               |    2 +
 src/UIElements/Qt4/Query/QtQueryList.hpp           |    6 +-
 src/UIElements/Qt4/Query/StringsQtQuery.cpp        |    2 +-
 src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp   |    2 +-
 src/UIElements/Qt4/Query/VectorsQtQuery.cpp        |    2 +-
 src/UIElements/TextUI/TextDialog.cpp               |    3 +-
 src/UIElements/TextUI/TextDialog.hpp               |    2 +-
 src/UIElements/TextUI/TextUIFactory.cpp            |    4 +-
 src/UIElements/TextUI/TextUIFactory.hpp            |    2 +-
 src/UIElements/UIFactory.hpp                       |    2 +-
 src/UIElements/Views/Qt4/Plotting/QSeisPlot.cpp    |    2 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp       |   17 -
 .../Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp       |    7 +-
 .../Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp       |    5 +
 .../Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp      |   91 +-
 src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp     |  136 +-
 src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp     |    6 +
 src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp      |  998 +-------
 src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp      |  130 +-
 src/UIElements/Views/Qt4/QtHomologyList.cpp        |   44 +-
 src/UIElements/Views/Qt4/QtMoleculeList.cpp        |    6 +-
 src/UIElements/Views/Qt4/QtToolBar.cpp             |   16 +-
 src/UIElements/Views/Qt4/QtToolBar.hpp             |   74 +-
 .../Views/Qt4/QtToolBar_QtFavoriteActions.cpp      |  199 ++
 src/World.cpp                                      |   47 +-
 src/builder.cpp                                    |    5 +-
 src/cleanUp.cpp                                    |    5 +
 src/documentation/constructs/filling.dox           |   14 +-
 src/documentation/tests/tests.dox                  |   14 +-
 src/molecule.cpp                                   |   11 -
 src/molecule.hpp                                   |   20 +-
 src/molecule_geometry.cpp                          |  194 +-
 src/moleculelist.cpp                               |   12 +-
 tests/Python/AllActions/options.dat                |    3 +-
 ...-analysis-dipole-correlation-discrete-angles.at |    6 +-
 .../testsuite-analysis-dipole-correlation-empty.at |    2 +-
 tests/regression/Atoms/Add/testsuite-atoms-add.at  |    4 +-
 .../post/tensid-undo.data                          |    0
 .../post/tensid.data                               |    0
 .../Filling/FillSurface/post/water_cube.xyz        |   80 +
 .../Filling/FillSurface/post/water_cylinder.xyz    |   98 +
 .../Filling/FillSurface/post/water_sphere.xyz      |   62 +
 .../Filling/FillSurface/post/water_undo.xyz        |    5 +
 .../pre/tensid.data                                |    0
 .../pre/tensid.potentials                          |    0
 tests/regression/Filling/FillSurface/pre/water.xyz |    5 +
 .../FillSurface/testsuite-fill-surface-cube.at     |  102 +
 .../FillSurface/testsuite-fill-surface-cylinder.at |  102 +
 .../testsuite-fill-surface-everywhere.at           |   46 +
 .../FillSurface/testsuite-fill-surface-micelle.at  |  105 +
 .../FillSurface/testsuite-fill-surface-nowhere.at  |   45 +
 .../FillSurface/testsuite-fill-surface-sphere.at   |  102 +
 .../Filling/FillVoidWithMolecule/post/propane.xyz  |   13 -
 .../Filling/FillVoidWithMolecule/post/tensid.data  | 2769 --------------------
 .../Filling/FillVoidWithMolecule/post/test.conf    | 1077 --------
 .../Filling/FillVoidWithMolecule/post/test.xyz     |  932 -------
 .../Filling/FillVoidWithMolecule/pre/tensid.data   |   59 -
 .../FillVoidWithMolecule/pre/tensid.potentials     | 1546 -----------
 .../Filling/FillVoidWithMolecule/pre/test.conf     |   83 -
 .../Filling/FillVoidWithMolecule/pre/water.data    |    4 -
 .../testsuite-fill-void-with-molecule.at           |   69 -
 .../testsuite-fill-void-with-tenside-molecule.at   |   57 -
 .../Filling/FillVolume/post/water_cylinder.xyz     |   14 +
 .../Filling/FillVolume/post/water_undo.xyz         |    5 +
 tests/regression/Filling/FillVolume/pre/water.xyz  |    5 +
 .../FillVolume/testsuite-fill-volume-cube.at       |   43 +
 .../FillVolume/testsuite-fill-volume-cylinder.at   |   92 +
 .../FillVolume/testsuite-fill-volume-everywhere.at |   43 +
 .../FillVolume/testsuite-fill-volume-nowhere.at    |   42 +
 .../FillVolume/testsuite-fill-volume-sphere.at     |   43 +
 .../Filling/FillWithMolecule/post/propane.xyz      |   13 -
 .../Filling/FillWithMolecule/post/test.conf        | 1089 --------
 .../Filling/FillWithMolecule/pre/test.conf         |   83 -
 .../testsuite-fill-with-molecule.at                |   72 -
 .../RegularGrid/post/solved_double_sles.data       |  708 +++---
 .../RegularGrid/post/solved_single_sles.data       | 1332 +++++-----
 ...=> testsuite-fill-regular-grid-with-surface.at} |    0
 ...ular-grid.at => testsuite-fill-regular-grid.at} |    0
 .../testsuite-molecules-fill-spherical-surface.at  |   57 -
 tests/regression/Filling/testsuite-filling.at      |   27 +-
 tests/regression/Makefile.am                       |   19 +-
 .../testsuite-options-invalid-commands.at          |   13 +-
 .../Options/Warranty/testsuite-options-warranty.at |    1 -
 .../Parser/Mpqc/testsuite-parser-mpqc-load.at      |    2 +-
 .../testsuite-set-random-number-distribution.at    |    8 +-
 .../Engine/testsuite-set-random-number-engine.at   |    8 +-
 215 files changed, 5391 insertions(+), 12269 deletions(-)
 create mode 100644 src/Actions/FillAction/FillVolumeAction.cpp
 create mode 100644 src/Actions/FillAction/FillVolumeAction.def
 create mode 100644 src/Actions/FillAction/FillVolumeAction.hpp
 create mode 100644 src/Actions/FillAction/SuspendInMoleculeAction.cpp
 create mode 100644 src/Actions/FillAction/SuspendInMoleculeAction.def
 create mode 100644 src/Actions/FillAction/SuspendInMoleculeAction.hpp
 delete mode 100644 src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp
 delete mode 100644 src/Actions/MoleculeAction/FillVoidWithMoleculeAction.def
 delete mode 100644 src/Actions/MoleculeAction/FillVoidWithMoleculeAction.hpp
 delete mode 100644 src/Actions/MoleculeAction/FillWithMoleculeAction.cpp
 delete mode 100644 src/Actions/MoleculeAction/FillWithMoleculeAction.def
 delete mode 100644 src/Actions/MoleculeAction/FillWithMoleculeAction.hpp
 delete mode 100644 src/Actions/MoleculeAction/SuspendInWaterAction.cpp
 delete mode 100644 src/Actions/MoleculeAction/SuspendInWaterAction.def
 delete mode 100644 src/Actions/MoleculeAction/SuspendInWaterAction.hpp
 create mode 100644 src/Filling/Inserter/SurfaceRandomInserter.cpp
 create mode 100644 src/Filling/Inserter/SurfaceRandomInserter.hpp
 create mode 100644 src/Filling/Preparators/BaseFillerPreparator.cpp
 create mode 100644 src/Filling/Preparators/BaseFillerPreparator.hpp
 create mode 100644 src/Filling/Preparators/BoxFillerPreparator.cpp
 create mode 100644 src/Filling/Preparators/BoxFillerPreparator.hpp
 create mode 100644 src/Filling/Preparators/ShapeSurfaceFillerPreparator.cpp
 create mode 100644 src/Filling/Preparators/ShapeSurfaceFillerPreparator.hpp
 create mode 100644 src/Filling/Preparators/ShapeVolumeFillerPreparator.cpp
 create mode 100644 src/Filling/Preparators/ShapeVolumeFillerPreparator.hpp
 create mode 100644 src/Parameters/Specifics/Value_atom.cpp
 create mode 100644 src/Parameters/Specifics/Value_atom.hpp
 create mode 100644 src/Parameters/Specifics/Value_element.cpp
 create mode 100644 src/Parameters/Specifics/Value_element.hpp
 create mode 100644 src/Parameters/Specifics/Value_molecule.cpp
 create mode 100644 src/Parameters/Specifics/Value_molecule.hpp
 create mode 100644 src/Parameters/Specifics/Value_string.cpp
 create mode 100644 src/Parameters/Specifics/Value_string.hpp
 create mode 100644 src/Parameters/Validators/getFlatListFromHierarchyOfValidators.hpp
 delete mode 100644 src/Parameters/Value_string.cpp
 delete mode 100644 src/Parameters/Value_string.hpp
 create mode 100644 src/UIElements/Menu/Qt4/QMenu_tooltip.hpp
 create mode 100644 src/UIElements/Views/Qt4/QtToolBar_QtFavoriteActions.cpp
 rename tests/regression/Filling/{SphericalSurface => FillSurface}/post/tensid-undo.data (100%)
 rename tests/regression/Filling/{SphericalSurface => FillSurface}/post/tensid.data (100%)
 create mode 100644 tests/regression/Filling/FillSurface/post/water_cube.xyz
 create mode 100644 tests/regression/Filling/FillSurface/post/water_cylinder.xyz
 create mode 100644 tests/regression/Filling/FillSurface/post/water_sphere.xyz
 create mode 100644 tests/regression/Filling/FillSurface/post/water_undo.xyz
 rename tests/regression/Filling/{SphericalSurface => FillSurface}/pre/tensid.data (100%)
 rename tests/regression/Filling/{SphericalSurface => FillSurface}/pre/tensid.potentials (100%)
 create mode 100644 tests/regression/Filling/FillSurface/pre/water.xyz
 create mode 100644 tests/regression/Filling/FillSurface/testsuite-fill-surface-cube.at
 create mode 100644 tests/regression/Filling/FillSurface/testsuite-fill-surface-cylinder.at
 create mode 100644 tests/regression/Filling/FillSurface/testsuite-fill-surface-everywhere.at
 create mode 100644 tests/regression/Filling/FillSurface/testsuite-fill-surface-micelle.at
 create mode 100644 tests/regression/Filling/FillSurface/testsuite-fill-surface-nowhere.at
 create mode 100644 tests/regression/Filling/FillSurface/testsuite-fill-surface-sphere.at
 delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/post/propane.xyz
 delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/post/tensid.data
 delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/post/test.conf
 delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/post/test.xyz
 delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/pre/tensid.data
 delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/pre/tensid.potentials
 delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/pre/test.conf
 delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/pre/water.data
 delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at
 delete mode 100644 tests/regression/Filling/FillVoidWithMolecule/testsuite-fill-void-with-tenside-molecule.at
 create mode 100644 tests/regression/Filling/FillVolume/post/water_cylinder.xyz
 create mode 100644 tests/regression/Filling/FillVolume/post/water_undo.xyz
 create mode 100644 tests/regression/Filling/FillVolume/pre/water.xyz
 create mode 100644 tests/regression/Filling/FillVolume/testsuite-fill-volume-cube.at
 create mode 100644 tests/regression/Filling/FillVolume/testsuite-fill-volume-cylinder.at
 create mode 100644 tests/regression/Filling/FillVolume/testsuite-fill-volume-everywhere.at
 create mode 100644 tests/regression/Filling/FillVolume/testsuite-fill-volume-nowhere.at
 create mode 100644 tests/regression/Filling/FillVolume/testsuite-fill-volume-sphere.at
 delete mode 100644 tests/regression/Filling/FillWithMolecule/post/propane.xyz
 delete mode 100644 tests/regression/Filling/FillWithMolecule/post/test.conf
 delete mode 100644 tests/regression/Filling/FillWithMolecule/pre/test.conf
 delete mode 100644 tests/regression/Filling/FillWithMolecule/testsuite-fill-with-molecule.at
 rename tests/regression/Filling/RegularGrid/{testsuite-molecules-fill-regular-grid-with-surface.at => testsuite-fill-regular-grid-with-surface.at} (100%)
 rename tests/regression/Filling/RegularGrid/{testsuite-molecules-fill-regular-grid.at => testsuite-fill-regular-grid.at} (100%)
 delete mode 100644 tests/regression/Filling/SphericalSurface/testsuite-molecules-fill-spherical-surface.at


hooks/post-receive
-- 
MoleCuilder


From git at ins.uni-bonn.de  Wed Sep 17 21:51:39 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Wed, 17 Sep 2014 21:51:39 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder annotated tag v1.4.8 created.
	v1.4.8
Message-ID: <20140917195139.CC7BE10000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "MoleCuilder".

The annotated tag, v1.4.8 has been created
        at  c6204d0e3a45cbcb6116e4a45ea9853eba248be5 (tag)
   tagging  7f6a2fc9f64c88371654df745552167f0e0e3a9c (commit)
  replaces  v1.4.7
 tagged by  Frederik Heber
        on  Wed Sep 17 21:39:28 2014 +0200

- Log -----------------------------------------------------------------
Valgrind-checked the code and eliminated all memory leaks.
First step of cleaning out old code (molecuilder_geometry and old fill Actions)
GUI is a lot more useful (empty dialogs do not show up, i.e. easy clicking with
	all selection actions, undo/redo, ..., bonds are properly updated when
	atoms move, tooltips for every option in dialogs, homology tab working,
	suffixes as filters in filedialogs)

This version contains the following branches:
7f6a2fc	Candidate_v1.4.8 (Fixes after merge and version)
8859b5e	GUI_Fixes (Lots of fixes to ease and enhance GUI usage)
5a9f4c1	Cleanup_old_code (throwing out old pieces of code, especially filler)
5524ae9	MemFixes (enable-valgrind now runs through without a glitch (except
	Python-related regression tests))

Frederik Heber (54):
      FIX: Process' dstor would always stop() even if not start()ed.
      FIX: FitPotentialAction's getFirstGraphwithSpecifiedElements() access key_end().
      FIX: Box::setM() did not use const ref as argument.
      FIX: regression test add atoms outside boundary had given boundary conditions wrong in arguments.
      FIX: Made checks in random number engine and distribution regression tests more robust.
      MEMFIX: World's homologies not deleted.
      MEMFIX: Mismatched delete in PdbParser::Save().
      MEMFIX: ActionQueue would loose memory when action failed.
      MEMFIX: RealSpaceMatrix's and MatrixContent's serialization leaked memory.
      MEMFIX: SaturationDistanceMaximizer::operator() did not delete Advocate.
      MEMFIX: PotentialRegistry's dstor forgot cleanup().
      MEMFIX: PartialNucleiChargeFitter lost memory.
      MEMFIX: Many analysis_correlation function allocated return map twice.
      MEMFIX: Tesselation::operator() did not free linkedlist.
      FIX: molecule::Translate() uses AtomSet directly.
      Added option keep-bondgraph to MolecularDynamicsAction and StructuralOptimizationAction.
      World::setTime() now only copies bond graph, does not re-create it.
      FIX: Removed some misleading output of CorrectBondDegreeAction.
      FIX: BondGraph::cleanAdjacencyList() killed bonds of time steps before.
      FIX: GLMoleculeObject_shape might use empty point list for tesselation.
      FIX: Added update mechanism to GLWorldScene when WorldTime changes.
      FileQtQuery retrieves valid suffixes from validators.
      FIX: molecule::Translate() used in CenterInBox(), CenterEdge(), CenterPeriodic(), and CenterAtVector().
      FIX: Changes to function signatures in molecule_geometry.
      Added FileSuffixValidator to all Actions where missing but appropriate.
      In QTUI empty dialogs no longer have to be confirmed.
      FIX: Querys now have own description as tooltip, not Action's.
      In QTUI Dialog window now has a meaningful title.
      QMenu extended for tooltips, but not working yet.
      FIX: new item is just to some default values in QtMoleculeList, filled later anway.
      FIX: FillRegularGridAction requires filler molecule at origin.
      Extracted filler preparing functionality from FillRegularGridAction.
      FIX: Renamed testsuite-molecules-fill-.. -> testsuite-fill-.. in Filling/.
      Added FillVolumeAction for filling a Shape's volume.
      Refactored FillSurfaceAction to also use FillerPreparators.
      Removed FillVoidWithMolecule and FillWithMolecule actions.
      Removed FillBoxWithMolecule(), FillVoidWithMolecule, and helper functions.
      Moved and renamed SuspendInWaterAction from Molecule.. to FillAction/SuspendInMoleculeAction.
      Removed PrepareClustersInWater().
      Removed lots of commented-out code from GLWorldView.
      FIX: QtQueryList now works with pointers, FileQtQuery gives name of file.
      FIX: QSeisPlotPage takes up all remaining space in QtHomologyList.
      FIX: QtHomologyList lacked use of FunctionModel::filter_t to split up arguments.
      Made ActionQueue observable.
      Added QtFavoriteActions to QtToolBar to spawn placeholder icons of most favorite Actions.
      MEMFIX: ActionQueue was not stopped() when argument parsing failed.
      MEMFIX: ElementDbAction would loose memory when parsing command-line arguments failed.
      DOCU: Update on test policy with respect to now working valgrind tests.
      Merge branch 'Cleanup_old_code' into stable
      Merge branch 'MemFixes' into stable
      Merge branch 'GUI_Fixes' into stable
      MEMFIX: Thrown ParserException causes mem leak in LoadAction
      FIX: CommandLineParser causes idling thread when parsing goes wrong.
      Set version to 1.4.8.

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From git at ins.uni-bonn.de  Thu Sep 18 00:26:22 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 18 Sep 2014 00:26:22 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.8
	deleted. v1.4.7-54-g4d966a0
Message-ID: <20140917222622.95B8C10000FA@jupiter.ins.uni-bonn.de>

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The branch, Candidate_v1.4.8 has been deleted
       was  4d966a045dba17945ab7e6433ebf4faea3d73b17

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4d966a045dba17945ab7e6433ebf4faea3d73b17 Set version to 1.4.8.
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From git at ins.uni-bonn.de  Thu Sep 18 00:27:09 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 18 Sep 2014 00:27:09 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch GUI_Fixes deleted.
	v1.4.7-18-g8859b5e
Message-ID: <20140917222709.431B310000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, GUI_Fixes has been deleted
       was  8859b5e80aaacf810ed6de2750789019357f0fa0

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8859b5e80aaacf810ed6de2750789019357f0fa0 Added QtFavoriteActions to QtToolBar to spawn placeholder icons of most favorite Actions.
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From git at ins.uni-bonn.de  Thu Sep 18 00:27:51 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 18 Sep 2014 00:27:51 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch MemFixes deleted.
	v1.4.7-17-g5524ae9
Message-ID: <20140917222751.828AF10000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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       was  5524ae96797a4fa7244c906512ec2bde76c952b3

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5524ae96797a4fa7244c906512ec2bde76c952b3 DOCU: Update on test policy with respect to now working valgrind tests.
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From git at ins.uni-bonn.de  Thu Sep 18 00:28:01 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 18 Sep 2014 00:28:01 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Cleanup_old_code
	deleted. v1.4.7-13-g5a9f4c1
Message-ID: <20140917222801.695E710000FA@jupiter.ins.uni-bonn.de>

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The branch, Cleanup_old_code has been deleted
       was  5a9f4c1e1caa72f88ad756fdaa11851f54a9426b

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5a9f4c1e1caa72f88ad756fdaa11851f54a9426b Removed lots of commented-out code from GLWorldView.
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From git at ins.uni-bonn.de  Thu Sep 18 23:59:32 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 18 Sep 2014 23:59:32 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch ThreadFixes deleted.
	v1.4.7-20-g2b11dfb
Message-ID: <20140918215932.AC68310000FA@jupiter.ins.uni-bonn.de>

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The branch, ThreadFixes has been deleted
       was  2b11dfbc1e1e35a26b0f0634b74d579dc3fc208b

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2b11dfbc1e1e35a26b0f0634b74d579dc3fc208b Cleaned up use of mutexes in ActionQueue.
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From git at ins.uni-bonn.de  Thu Sep 18 23:59:38 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Thu, 18 Sep 2014 23:59:38 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch ThreadFixes created.
	v1.4.7-20-gca890d1
Message-ID: <20140918215938.1613A10000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, ThreadFixes has been created
        at  ca890d10159865475183bd08e46c1d304c75cc3f (commit)

- Log -----------------------------------------------------------------
commit ca890d10159865475183bd08e46c1d304c75cc3f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 3 21:26:17 2014 +0200

    Cleaned up use of mutexes in ActionQueue.
    
    - tempqueue now has its own mutex.
    - more often using lock_guard.
    - run_thread_isIdle has own mutex.

commit 13102c09392ef451c7547ec206917e96beeb1fad
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 3 19:21:08 2014 +0200

    Added extra flag run_thread_running to ActionQueue.
    
    - helgrind admonished race conditions when thread is joined. This did not fix
      them but should be safer as we cannot know whether the other thread has
      already been started when suddenly shutting down molecuilder due to an
      exception.

commit bc2d4676ddd23758665398fbacb74e40e7fdb45b
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Aug 29 11:46:02 2014 +0200

    THREADFIX: Fixed ActionQueue with respect to mutex and threads.
    
    - run_thread is now last member variable, hence started after all other
      variables are initialized.
    - separated accesses to queues and to run_thread_isIdle flag. Also renamed
      its mutex for easier association with it.

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From git at ins.uni-bonn.de  Fri Sep 26 17:39:25 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Fri, 26 Sep 2014 17:39:25 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch
	Fix_ConvexizeNonconexEnvelope created. v1.4.8-30-gab72314
Message-ID: <20140926153925.A10A410000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
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The branch, Fix_ConvexizeNonconexEnvelope has been created
        at  ab72314934e071f1c33d4d2875f9d27458fb67da (commit)

- Log -----------------------------------------------------------------
commit ab72314934e071f1c33d4d2875f9d27458fb67da
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 21:13:43 2014 +0200

    Changed verbosities in tesselation a lot to make readable.

commit 743052c22b9d7f7591cac44bd5eb2e484a5c3e42
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:20 2014 +0200

    FIX: Changed all performCriticalExit() into ASSERT() in tesselation.

commit d4f9bb3aba23969df122e85d3f5307a0398e5c3f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:26:03 2014 +0200

    Changed some verbosities in Tesselation code.

commit a07e7053630cf9faa4f5fc18481901cc4f79ab96
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:24:52 2014 +0200

    FIX: RemoveTesselationLine() needs to erase line from OpenLines if present.

commit 8e3d9d4f8f83fa748239e028a866abd8ab8c70d0
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 20:23:50 2014 +0200

    FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle when polygon is not convex.

commit 10a01718c3a6190cfc9de345527be832011b1f87
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:25:23 2014 +0200

    FIX: AddTesselationLine() would onl work in initial tesselation phase.
    
    - the CandidateForTesselation instance is NULL when we convexize and this
      was not correctly processed by AddTesselationLine().

commit e13991dce439602624fbb51421d9bf3c0a816396
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 25 18:24:30 2014 +0200

    Added SphereRadius parameter to ConvexEnvelopeAction.

commit 128616612a611878bc0a942bbc2f1eecab5d0c9a
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Sep 23 18:14:18 2014 +0200

    FIX: Setting ActionQueue::_lastchangedaction without heeding whether Action failed is bad.
    
    - causes segfault when notification informs about change and _lastchangeaction
      is still NULL (as the very first Action failed).
    - we now only notify when action succeeded.

commit 56eee6e652088e82274fd47b6fd2b3b70e898feb
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Mon Sep 22 22:10:11 2014 +0200

    FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when initialized.

commit 78c9509cba8ec6569d3fee2987607785743b7e09
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 19 13:19:18 2014 +0200

    FIX: QtHomologyList's plot widget was too high (and fixed).
    
    - also the sizes of splitter's children in QtHomologyList are now stored to
      settings (as QsizePolicy does not have an effect on a splitter).

commit 71350daef4a36bbd039aa43a5712363fddfc5a00
Merge: 14bede3 c7fe90c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 19 09:13:05 2014 +0200

    Merge branch 'Experiment_Amylose_Water' into Candidate_v1.4.9
    
    Conflicts:
    	doc/userguide/userguide.xml
    	tests/regression/Atoms/testsuite-atoms.at
    
    - mirror-atoms and translate-to-origins occupied the same places.

commit 14bede3ba3e8e2630b00858a76285e0e0439b26a
Merge: 5340768 46ce1c8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 19 09:11:02 2014 +0200

    Merge branch 'DynamicMolecules' into Candidate_v1.4.9

commit 5340768e903e79d978c07f327466f51ba993a139
Merge: 2ed3bf3 9d1320c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 19 09:10:10 2014 +0200

    Merge branch 'Refactoring_PotentialActions' into Candidate_v1.4.9

commit 2ed3bf3dd38da578e40e717928f565e66746d252
Merge: 7acbfc4 bbf6dcd
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 19 09:10:04 2014 +0200

    Merge branch 'MirrorAtoms' into Candidate_v1.4.9

commit 7acbfc4fee584acd54942911e6d4b9c73149b2c7
Merge: 9bce964 054d47f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 19 09:09:53 2014 +0200

    Merge branch 'ActionFixes' into Candidate_v1.4.9

commit bbf6dcd010a0439f2e1a441678550e5a56e1cf30
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Wed Sep 10 01:55:39 2014 +0200

    Added AtomMirrorAction.
    
    - also added regression tests.

commit 9d1320cc5a22b299fc35b50bb519d8bd8b13bc21
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 12 09:54:12 2014 +0200

    Extracted SavePotentialsAction.
    
    - PotentialTrainer::StorePotentials removed.
    - Fit...Actions do not store anymore.
    - TESTFIX: potential regression tests now use save-potentials and compare
      against stored file.

commit 5c6b432e38763ef95f591b8dae5078375f60c46c
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Fri Sep 12 09:39:58 2014 +0200

    Extracted ParsePotentialsAction from FitCompoundPotentialAction.

commit 21c1c5cb23b27248af841d0fb4f026616b41b8c5
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 11 22:38:05 2014 +0200

    Split FitPotentialAction into two actions.
    
    - FitPotentialAction fits just a single potential.
    - new FitCompoundPotentialAction fits via a potential file.
    - PotentialTrainer contains all helper functions and common code.

commit 46ce1c8a9f9a6af80b7fcf736dcf57f11b47f8b7
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 17 20:30:46 2014 +0200

    FIX: World::setTime() now first copies Bondgraph and then sets the time.
    
    - thus we do not cause GUI updates with each addBond().

commit 8cc22fe4af9577450a3d00a92ea000018b14b366
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 17 00:56:59 2014 +0200

    Changed how trajectories are stored, not as vecor but as map.
    
    - AtomInfo and atom_bondedparticleinfo now store map<unsigned int, ...> instead
      of vector<...>.
    - UpdateSteps() -> UpdateStep(unsigned int), same with RemoveSteps() and
      AppendTrajectorySteps() and RemoveTrajectorySteps().
    - made changes necessary to UndoRedoHelpers and two Actions.
    - TESTFIX: AtomObserverUnitTest failed as we longer "notify" in case already
      set element is set again. We now check that setType() sets to different
      element.

commit c7fe90cd467a73a0ef32b5c631534b2928c0b926
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Aug 14 22:03:53 2014 +0200

    Added TranslateToOriginAction.
    
    - also added regression test.

commit f4b626a1fbf68b80e642bace1770e5577aeed6d8
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Tue Aug 26 10:48:59 2014 +0200

    Added AverageMoleculeForceAction for measuring average force acting on a molecule.

commit 7a7b3408459dae333637248d2b3e0bebed301975
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Aug 17 12:10:08 2014 +0200

    FIX: atom's copy cstor does not need to copy positions, ... again.

commit 054d47f3558f3549e6480280882111c4df74ad9f
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Thu Sep 11 09:31:52 2014 +0200

    FIX: (Not)AtomByIdAction would fail with assert if not atoms are present.
    
    - none are selected, we just fail the Action but removed assert.

commit 9bce96471db8bac23510c29ddaa7dbcabf15d765
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 14 21:26:46 2014 +0200

    DOCU: Fixed all missing links in userguide.
    
    - each section now has a linkname.

commit f73e0644af36b981af22685b57300f77cb7b0937
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 14 20:25:06 2014 +0200

    DOCU: Added all missing Actions to userguide.
    
    - removed XFAIL from associated CodeChecks test.

commit c62e275561001d2ecd22b8489ac47810fd64e5ce
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 14 18:23:41 2014 +0200

    Added CodeChecks test that every action appears in the userguide.
    
    - test is marked as XFAIL for the moment.

commit 2a6d8c7977c1f749091ead256bcca349538a8b59
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 14 20:24:38 2014 +0200

    DOCUFIX: Doyxygen formula was broken in SaturationDistanceMaximizer.

commit ced7f04bae3c2939e0888dfb7559e4b0f342a808
Author: Frederik Heber <heber at ins.uni-bonn.de>
Date:   Sun Sep 14 20:24:23 2014 +0200

    VersionAction also prints to log, not only to status.

-----------------------------------------------------------------------


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From git at ins.uni-bonn.de  Fri Sep 26 18:37:30 2014
From: git at ins.uni-bonn.de (git repository hosting)
Date: Fri, 26 Sep 2014 18:37:30 +0200 (CEST)
Subject: [Molecuilder-devel] [SCM] MoleCuilder branch Candidate_v1.4.9
	created. v1.4.8-21-g78c9509
Message-ID: <20140926163730.750E410000FA@jupiter.ins.uni-bonn.de>

This is an automated email from the git hooks/post-receive script. It was
generated because a ref change was pushed to the repository containing
the project "MoleCuilder".

The branch, Candidate_v1.4.9 has been created
        at  78c9509cba8ec6569d3fee2987607785743b7e09 (commit)

- Log -----------------------------------------------------------------
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